The NCBI BioCollections Database

Sharma, Shobha; Ciufo, Stacy; Starchenko, Elena; Darji, Dakshesh; Chlumsky, Larry; Karsch-Mizrachi, Ilene; Schoch, Conrad L.

doi:10.1093/database/bay006

Cited by 64 publications

(57 citation statements)

References 16 publications

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“…Six of them were from our previous research (Jiang et al, 2019) and 19 of them were from the other researcher's report (Wu et al, 2018). The data were deposited in BIG Data Center (BIG Data Center Members, 2018) and the National Center for Biotechnology Information [NCBI (Sharma et al, 2018)]. Their accession numbers are shown in Table 1.…”

Section: Methodsmentioning

confidence: 99%

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

Jiang¹,

An²,

Wang³

et al. 2019

J. Amer. Soc. Hort. Sci.

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Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

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Section: Methodsmentioning

confidence: 99%

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

Jiang¹,

An²,

Wang³

et al. 2019

J. Amer. Soc. Hort. Sci.

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“…The pipeline mines OR gene and pseudogene sequences out of any given genome to obtain the complete OR repertoire of that species, and is based on a series of TBLASTN searches as explained in detail in [11]. The OR repertoires (Table 1) were compared to relevant publications and public resources including Mouse Genome Informatics (MGI, [42]), Rat Genome Database (RGD, [43]), The Zebrafish Information Network (ZFIN, [44]), as well as Ensembl [45] and NCBI [46]. The sizes of the identified repertoires are in good agreement with those resources, as well as with published studies [19,20,47].…”

Section: Methodsmentioning

confidence: 99%

A unified nomenclature for vertebrate olfactory receptors

Olender

Jones²,

Twik

et al. 2019

Preprint

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Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5 . Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~50% in dog and cow and to ~30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

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“…Asian yellow people were obtained from the TCGA database [3]. Immune gene names were obtained from the IMMPORT database, and immune genes were screened from the downloaded data [4].…”

Section: Get Relevant Data From Network Database the Coad Gene Exprementioning

confidence: 99%

Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms

Chen

et al. 2020

Preprint

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Background: Colon adenocarcinoma(COAD) is a type of gastrointestinal tumor with a high degree of malignancy, and its immunotherapy method has been stagnant. Recently, with the development of network databases and the development of bioinformatics tools, we can analyze the data in the current database to find out which genes may be the target of immunotherapy for COAD.Methods: We use various codes and packages of R language to analyze the downloaded data, construct a riskScore model of immune genes and clinical data, and use Cox regression analysis to explore the clinical relationship between riskScore and COAD.Results: We found that seven immune genes associated with the survival prognosis of COAD were related to the construction of a riskScore model. And Cox regression analysis found that there was clinical significance and statistical significance between the riskScore model and clinical data of COAD. Some traditional immune microenvironment cells also increase their cell content with the increase of riskScore.Conclusions: We found 7 immune genes (SLC10A2, CXCL3, IGHV5-51, INHBA, STC1, UCN and OXTR) that affect the clinical prognosis of COAD patients and can construct a riskScore model. It may be a target for future COAD immunotherapy.

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The NCBI BioCollections Database

Cited by 64 publications

References 16 publications

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

A unified nomenclature for vertebrate olfactory receptors

Prediction and identification of immune genes related to the prognosis of patients with colon adenocarcinoma and its mechanisms

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